Multiple sequence alignment - TraesCS3B01G030300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G030300 chr3B 100.000 2872 0 0 479 3350 13906179 13903308 0.000000e+00 5304.0
1 TraesCS3B01G030300 chr3B 80.328 488 55 17 479 947 259244110 259243645 6.930000e-87 331.0
2 TraesCS3B01G030300 chr3B 100.000 148 0 0 1 148 13906657 13906510 1.180000e-69 274.0
3 TraesCS3B01G030300 chr3B 88.073 218 26 0 3094 3311 225255844 225256061 3.320000e-65 259.0
4 TraesCS3B01G030300 chr3B 94.444 144 8 0 4 147 259244272 259244129 4.350000e-54 222.0
5 TraesCS3B01G030300 chr3B 90.588 170 12 1 703 868 259244310 259244479 4.350000e-54 222.0
6 TraesCS3B01G030300 chr3B 86.339 183 19 3 688 870 13906648 13906824 9.480000e-46 195.0
7 TraesCS3B01G030300 chr3A 87.593 669 55 6 2710 3350 715554781 715554113 0.000000e+00 750.0
8 TraesCS3B01G030300 chr3A 87.225 227 29 0 3094 3320 738332843 738332617 3.320000e-65 259.0
9 TraesCS3B01G030300 chr5A 87.126 668 58 6 2711 3350 8500752 8500085 0.000000e+00 732.0
10 TraesCS3B01G030300 chr4A 82.665 623 80 18 2711 3314 201632816 201632203 8.230000e-146 527.0
11 TraesCS3B01G030300 chr4A 84.483 406 41 13 2711 3097 536785524 536785122 6.780000e-102 381.0
12 TraesCS3B01G030300 chr4A 78.808 453 70 19 2230 2667 681609357 681609798 7.080000e-72 281.0
13 TraesCS3B01G030300 chr5B 82.287 621 81 17 2714 3314 34783280 34782669 8.290000e-141 510.0
14 TraesCS3B01G030300 chr5B 84.892 278 31 9 523 793 248753706 248753979 1.530000e-68 270.0
15 TraesCS3B01G030300 chr5B 83.849 291 20 12 689 953 248753539 248753250 5.550000e-63 252.0
16 TraesCS3B01G030300 chr5B 84.556 259 30 6 705 953 248753920 248754178 7.180000e-62 248.0
17 TraesCS3B01G030300 chr5B 93.007 143 10 0 1 143 248753531 248753673 3.390000e-50 209.0
18 TraesCS3B01G030300 chr5B 87.681 138 11 2 816 947 679821262 679821125 4.480000e-34 156.0
19 TraesCS3B01G030300 chr5B 84.932 146 17 4 812 952 68422887 68422742 3.480000e-30 143.0
20 TraesCS3B01G030300 chr4D 81.947 637 79 24 2710 3316 43264329 43263699 1.070000e-139 507.0
21 TraesCS3B01G030300 chr4D 80.938 341 36 14 2710 3033 477534482 477534154 3.340000e-60 243.0
22 TraesCS3B01G030300 chrUn 94.521 292 16 0 957 1248 32344440 32344731 5.100000e-123 451.0
23 TraesCS3B01G030300 chrUn 96.907 97 3 0 2130 2226 32344727 32344823 2.670000e-36 163.0
24 TraesCS3B01G030300 chr2B 91.746 315 24 2 479 793 601205763 601206075 1.430000e-118 436.0
25 TraesCS3B01G030300 chr2B 92.213 244 13 3 2414 2651 29705987 29706230 1.150000e-89 340.0
26 TraesCS3B01G030300 chr2B 85.886 333 28 6 479 793 334699625 334699956 1.490000e-88 337.0
27 TraesCS3B01G030300 chr2B 86.364 308 23 2 479 786 694048110 694048398 5.390000e-83 318.0
28 TraesCS3B01G030300 chr2B 72.361 1165 251 52 1106 2222 17503174 17502033 5.430000e-78 302.0
29 TraesCS3B01G030300 chr2B 72.208 1137 228 48 1142 2222 17515160 17514056 5.510000e-68 268.0
30 TraesCS3B01G030300 chr2B 89.524 210 16 4 2453 2658 691266679 691266472 9.220000e-66 261.0
31 TraesCS3B01G030300 chr2B 80.060 331 48 14 523 842 217801328 217801005 2.600000e-56 230.0
32 TraesCS3B01G030300 chr2B 71.707 1078 216 55 1197 2218 17444261 17445305 5.630000e-53 219.0
33 TraesCS3B01G030300 chr2B 93.750 144 9 0 1 144 601205601 601205744 2.020000e-52 217.0
34 TraesCS3B01G030300 chr2B 93.662 142 9 0 1 142 334699461 334699602 2.620000e-51 213.0
35 TraesCS3B01G030300 chr2B 81.315 289 31 11 689 958 601205609 601205325 2.620000e-51 213.0
36 TraesCS3B01G030300 chr2B 94.161 137 8 0 11 147 39881080 39880944 3.390000e-50 209.0
37 TraesCS3B01G030300 chr2B 92.414 145 11 0 1 145 694047946 694048090 1.220000e-49 207.0
38 TraesCS3B01G030300 chr2B 92.908 141 10 0 5 145 453795701 453795841 4.380000e-49 206.0
39 TraesCS3B01G030300 chr2B 79.336 271 44 11 1144 1411 17144072 17144333 2.660000e-41 180.0
40 TraesCS3B01G030300 chr2B 85.294 136 12 3 1278 1411 5782141 5782012 2.100000e-27 134.0
41 TraesCS3B01G030300 chr1B 87.705 366 37 6 481 842 567761980 567762341 1.440000e-113 420.0
42 TraesCS3B01G030300 chr1B 90.614 277 25 1 504 779 587809215 587808939 1.900000e-97 366.0
43 TraesCS3B01G030300 chr1B 84.556 259 30 5 705 953 567762261 567762519 7.180000e-62 248.0
44 TraesCS3B01G030300 chr1B 83.137 255 28 7 703 952 587809402 587809646 5.630000e-53 219.0
45 TraesCS3B01G030300 chr6D 85.230 413 36 16 2256 2657 454211326 454210928 5.210000e-108 401.0
46 TraesCS3B01G030300 chr6D 83.538 407 46 12 2709 3097 216863194 216862791 8.840000e-96 361.0
47 TraesCS3B01G030300 chr6D 85.401 137 18 2 479 615 47676996 47677130 1.250000e-29 141.0
48 TraesCS3B01G030300 chr7D 83.784 407 45 12 2709 3097 475721650 475721247 1.900000e-97 366.0
49 TraesCS3B01G030300 chr7D 72.561 1148 242 35 1122 2222 21773849 21774970 1.170000e-79 307.0
50 TraesCS3B01G030300 chr7D 82.353 340 41 12 2711 3033 582519853 582519516 9.150000e-71 278.0
51 TraesCS3B01G030300 chr1D 92.742 248 14 3 2414 2657 486401898 486401651 4.110000e-94 355.0
52 TraesCS3B01G030300 chr2A 73.054 1169 236 51 1106 2222 11983249 11982108 1.150000e-89 340.0
53 TraesCS3B01G030300 chr6B 90.800 250 16 5 2414 2657 47929207 47929455 8.960000e-86 327.0
54 TraesCS3B01G030300 chr6B 86.014 286 20 7 2709 2974 134815005 134815290 4.230000e-74 289.0
55 TraesCS3B01G030300 chr6B 88.073 218 26 0 3094 3311 18451904 18452121 3.320000e-65 259.0
56 TraesCS3B01G030300 chr6B 93.662 142 9 0 4 145 687410826 687410685 2.620000e-51 213.0
57 TraesCS3B01G030300 chr6B 88.194 144 16 1 490 633 153675289 153675431 1.600000e-38 171.0
58 TraesCS3B01G030300 chr5D 90.361 249 20 3 2414 2658 79640498 79640250 1.160000e-84 324.0
59 TraesCS3B01G030300 chr5D 82.111 341 42 12 2710 3033 298522233 298521895 1.180000e-69 274.0
60 TraesCS3B01G030300 chr5D 78.088 502 53 24 479 952 545817341 545817813 7.130000e-67 265.0
61 TraesCS3B01G030300 chr2D 92.718 206 11 3 2456 2657 609295474 609295679 9.090000e-76 294.0
62 TraesCS3B01G030300 chr7B 87.225 227 29 0 3094 3320 99795708 99795482 3.320000e-65 259.0
63 TraesCS3B01G030300 chr7B 87.225 227 29 0 3094 3320 125247760 125247534 3.320000e-65 259.0
64 TraesCS3B01G030300 chr7B 87.225 227 29 0 3094 3320 125283815 125283589 3.320000e-65 259.0
65 TraesCS3B01G030300 chr7B 88.073 218 26 0 3094 3311 628353730 628353947 3.320000e-65 259.0
66 TraesCS3B01G030300 chr7B 86.784 227 30 0 3094 3320 125317696 125317470 1.540000e-63 254.0
67 TraesCS3B01G030300 chr7B 76.600 500 81 26 479 952 73897116 73897605 3.340000e-60 243.0
68 TraesCS3B01G030300 chr7B 82.917 240 37 3 2422 2657 22716499 22716260 2.620000e-51 213.0
69 TraesCS3B01G030300 chr7B 79.832 119 20 4 2242 2357 700894371 700894254 2.140000e-12 84.2
70 TraesCS3B01G030300 chr4B 87.500 224 27 1 3094 3316 30592902 30593125 1.190000e-64 257.0
71 TraesCS3B01G030300 chr7A 92.571 175 9 3 2487 2657 1475882 1475708 7.180000e-62 248.0
72 TraesCS3B01G030300 chr7A 71.603 1148 253 40 1122 2222 22198099 22199220 2.580000e-61 246.0
73 TraesCS3B01G030300 chr7A 86.164 159 16 6 2234 2389 1476126 1475971 2.070000e-37 167.0
74 TraesCS3B01G030300 chr7A 84.906 159 19 5 2234 2389 1476539 1476383 4.480000e-34 156.0
75 TraesCS3B01G030300 chr7A 86.301 146 14 3 812 953 105425657 105425800 1.610000e-33 154.0
76 TraesCS3B01G030300 chr3D 95.556 135 6 0 11 145 300711890 300711756 2.020000e-52 217.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G030300 chr3B 13903308 13906657 3349 True 2789.000000 5304 100.0000 1 3350 2 chr3B.!!$R1 3349
1 TraesCS3B01G030300 chr3B 259243645 259244272 627 True 276.500000 331 87.3860 4 947 2 chr3B.!!$R2 943
2 TraesCS3B01G030300 chr3A 715554113 715554781 668 True 750.000000 750 87.5930 2710 3350 1 chr3A.!!$R1 640
3 TraesCS3B01G030300 chr5A 8500085 8500752 667 True 732.000000 732 87.1260 2711 3350 1 chr5A.!!$R1 639
4 TraesCS3B01G030300 chr4A 201632203 201632816 613 True 527.000000 527 82.6650 2711 3314 1 chr4A.!!$R1 603
5 TraesCS3B01G030300 chr5B 34782669 34783280 611 True 510.000000 510 82.2870 2714 3314 1 chr5B.!!$R1 600
6 TraesCS3B01G030300 chr5B 248753531 248754178 647 False 242.333333 270 87.4850 1 953 3 chr5B.!!$F1 952
7 TraesCS3B01G030300 chr4D 43263699 43264329 630 True 507.000000 507 81.9470 2710 3316 1 chr4D.!!$R1 606
8 TraesCS3B01G030300 chr2B 17502033 17503174 1141 True 302.000000 302 72.3610 1106 2222 1 chr2B.!!$R2 1116
9 TraesCS3B01G030300 chr2B 17514056 17515160 1104 True 268.000000 268 72.2080 1142 2222 1 chr2B.!!$R3 1080
10 TraesCS3B01G030300 chr2B 17444261 17445305 1044 False 219.000000 219 71.7070 1197 2218 1 chr2B.!!$F2 1021
11 TraesCS3B01G030300 chr1B 567761980 567762519 539 False 334.000000 420 86.1305 481 953 2 chr1B.!!$F2 472
12 TraesCS3B01G030300 chr7D 21773849 21774970 1121 False 307.000000 307 72.5610 1122 2222 1 chr7D.!!$F1 1100
13 TraesCS3B01G030300 chr2A 11982108 11983249 1141 True 340.000000 340 73.0540 1106 2222 1 chr2A.!!$R1 1116
14 TraesCS3B01G030300 chr7A 22198099 22199220 1121 False 246.000000 246 71.6030 1122 2222 1 chr7A.!!$F1 1100


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
635 636 0.106419 AGTTTGGGCGGGAAAGACAA 60.106 50.0 0.0 0.0 0.0 3.18 F
1539 1657 0.035439 CCGTTTGCTCCCAGGTACAT 60.035 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 1979 0.034756 CACACCACCAACGATCCTGA 59.965 55.0 0.0 0.0 0.00 3.86 R
2469 2650 0.097674 GTCGATGTTGATGCAGTGGC 59.902 55.0 0.0 0.0 41.68 5.01 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.